As a method for detecting a nucleic acid molecule having a specific target nucleic acid sequence, a hybridization method using a probe having a nucleotide sequence complementary to the target nucleic acid sequence has been widely used. In the hybridization method, a probe having a nucleotide sequence complementary to the target nucleic acid sequence is prepared, and only a sample having a nucleotide sequence complementary to the nucleotide sequence of the probe is hybridized thereto with high selectivity. As a means for detecting a hybrid formed as a result of the hybridization, a method of labeling a probe nucleic acid with a radioisotope, a method of labeling a probe nucleic acid with a fluorescent substance, a method using a chemiluminescent reagent, and the like are applied. Fluorescent substances which can be used in the labeling of a nucleic acid include fluorescein, tetramethylrhodamine, Cy3, Cy5, and the like. A fluorescent nucleic acid probe labeled with such fluorescent substance has a high background fluorescence signal. Thus, it has been difficult to carry out highly sensitive measurement using such probe.